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https://github.com/PacificBiosciences/pbcopper

Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.

Proper citation: pbcopper (RRID:SCR_024152) Copy   

•   Source: SciCrunch Registry

https://harvest.readthedocs.io/en/latest/content/parsnp.html

Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

Proper citation: Parsnp (RRID:SCR_024153) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html

Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.

Proper citation: PDB2PQR (RRID:SCR_024155) Copy   

•   Source: SciCrunch Registry

https://github.com/sib-swiss/pftools3

Software suite of tools to build and search generalized profiles.

Proper citation: PfTools (RRID:SCR_024158) Copy   

•   Source: SciCrunch Registry

https://jydu.github.io/physamp/

Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.

Proper citation: PhySamp (RRID:SCR_024159) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/parsinsert/

Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.

Proper citation: ParsInsert (RRID:SCR_024163) Copy   

•   Source: SciCrunch Registry

https://github.com/bxlab/bx-python

Software Python library and associated set of scripts for rapid implementation of genome scale analyses.

Proper citation: python-bx (RRID:SCR_024202) Copy   

•   Source: SciCrunch Registry

https://github.com/RoelofBerg/limereg

Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.

Proper citation: limereg (RRID:SCR_024097) Copy   

•   Source: SciCrunch Registry

https://neobio.sourceforge.net/

Software library of sequence alignment algorithms implemented in Java.

Proper citation: NeoBio (RRID:SCR_024131) Copy   

•   Source: SciCrunch Registry

http://murasaki.dna.bio.keio.ac.jp/wiki/

Software language-theory based homology detection tool across multiple large genomes.

Proper citation: Murasaki (RRID:SCR_024132) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/books/NBK179288/

Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.

Proper citation: Entrez Direct (RRID:SCR_024136) Copy   

•   Source: SciCrunch Registry

https://doua.prabi.fr/software/njplot

Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

Proper citation: NJplot (RRID:SCR_024137) Copy   

•   Source: SciCrunch Registry

https://github.com/xdf-modules/libxdf

Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.

Proper citation: Libxdf (RRID:SCR_024096) Copy   

•   Source: SciCrunch Registry

https://github.com/mroosmalen/nanosv

Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

Proper citation: NanoSV (RRID:SCR_024127) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/NanoPlot

Software package as plotting tool for long read sequencing data and alignments.

Proper citation: NanoPlot (RRID:SCR_024128) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/OBITools/

Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.

Proper citation: OBITools (RRID:SCR_024141) Copy   

•   Source: SciCrunch Registry

https://www.orthanc-server.com/

Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.

Proper citation: Orthanc (RRID:SCR_024145) Copy   

•   Source: SciCrunch Registry

https://www.rostlab.org/owiki/index.php/Norsnet

Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data.

Proper citation: NORSnet (RRID:SCR_024146) Copy   

•   Source: SciCrunch Registry

http://www.opensurgsim.org/

Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers.

Proper citation: OpenSurgSim (RRID:SCR_024147) Copy   

•   Source: SciCrunch Registry

http://openigtlink.org/

Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.

Proper citation: OpenIGTLink (RRID:SCR_024148) Copy   

•   Source: SciCrunch Registry